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ОбложкаSeshasayee A.S.N. Bacterial genomics: genome organization and gene expression tools. - Delhi: Cambridge university press, 2015. - xiv, 211 p.: ill. - Bibliogr. in the foot-notes. - Ind.: p.207-211. - ISBN 978-1-107-07983-0
Шифр: (И/Е4-S49) 02
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
List of Figures ................................................ ix
Acknowledgements ............................................. xiii
1  Introduction: Bacterial Genomes and Gene Expression .......... 1
2  Comparative Genomics in the Era of Sanger Sequencing ......... 4
   2.1  Introduction ............................................ 4
   2.2  The process of assembling and annotating bacterial
        genomes ................................................. 6
        2.2.1  Genome assembly and gap closure .................. 7
        2.2.2  Genome-scale computational identification of
               features ......................................... 8
        2.2.3  Annotating genes with functions ................. 13
   2.3  Case studies ........................................... 16
        2.3.1  The Escherichia coli complex and large-scale
               horizontal gene acquisition ..................... 16
        2.3.2  Genome reduction in intracellular pathogens,
               endosymbionts and marine α-proteobacteria ....... 20
        2.3.3  The dynamic genomes of Helicobacter pylori and
               Campylobacter jejuni ............................ 26
   2.4  Some lessons learnt from studying 2,000 bacterial
        genomes ................................................ 27
        2.4.1  Genome size ..................................... 28
        2.4.2  Coding density .................................. 29
        2.4.3  Gene order conservation ......................... 30
        2.4.4  Comparative genomics of gene functions:
               Systematic annotation ........................... 31
        2.4.5  Comparative genomics of gene functions:
               Scaling laws .................................... 33
   Summary ..................................................... 35
3  Studying Bacterial Genome Variation with Microarrays ........ 36
   3.1  Introduction ........................................... 36
   3.2  DNA microarrays: The concept ........................... 36
   3.3  DNA microarrays: From fluorescence intensities to
        information ............................................ 38
        3.3.1  Background correction ........................... 39
        3.3.2  Normalisation ................................... 41
        3.3.3  Differences in signal from the same probe
               between two samples ............................. 44
   3.4  Comparative genome hybridisation and bacterial
        phylogenomics .......................................... 45
   3.5  Case studies ........................................... 46
        3.5.1  Comparative genome hybridisation studies of
               Escherichia coli ................................ 47
        3.5.2  Comparative genome hybridisation studies of
               Staphylococcus aureus ........................... 52
        3.5.3  Comparative genome hybridisation studies of
               Helicobacter pylori ............................. 56
   Summary ..................................................... 59
4  Studying Bacterial Genomes using Next-Generation
   Sequencing .................................................. 60
   4.1  Introduction ........................................... 60
   4.2  Next-generation sequencing technologies ................ 61
        4.2.1  Template preparation strategies ................. 62
        4.2.2  Sequencing strategies ........................... 64
   4.3  Sequencing data processing for genome sequencing
        and re-sequencing ...................................... 66
        4.3.1  Genome assembly ................................. 66
        4.3.2  Aligning short reads to long genomes ............ 70
   4.4  Case studies ........................................... 73
        4.4.1  Pyrosequencing-enabled complete genome
               sequence of Acinetobacter baumanii .............. 74
        4.4.2  On the track of pandemics: The genome of the
               aetiological agent of Black Death ............... 75
        4.4.3  From community genomes to complete genomes to
               single-cell genomes ............................. 80
        4.4.4  Bacteria evolving in the laboratory ............. 84
        4.4.5  Bacteria evolving in their biotic hosts ......... 86
   Summary ..................................................... 88
5  Genome-Scale Analysis of Gene Expression and its
   Regulation in Bacteria ...................................... 89
   5.1  Introduction ........................................... 89
   5.2  The process of transcription and the regulation of
        its initiation: An overview ............................ 90
   5.3  Measuring gene expression on a genomic scale:
        Technologies ........................................... 99
   5.4  Next-generation sequencing for gene expression
        measurements: Data analysis ........................... 101
        5.4.1  Transcriptome assembly ......................... 104
        5.4.2  Measuring gene expression levels ............... 110
   5.5  Gene expression at high temporal resolution using
        fluorescent reporters ................................. 114
   5.6  Constructing transcriptional regulatory networks:
        СЫР-chip and ChlP-seq ................................. 117
   5.7  Case studies .......................................... 122
        5.7.1  Experimental annotation of bacterial genomes ... 122
        5.7.2  Bioinformatic analysis of bacterial promoters .. 129
        5.7.3  DNA topology and its interplay with gene
               expression ..................................... 134
        5.7.4  RNA polymerase occupancy and the a-factors ..... 145
        5.7.5  Transcription factors and transcriptional
               regulatory networks ............................ 154
        5.7.6  Transcriptional control by the small-molecule
               alarmone ppGpp ................................. 186
        5.7.7  RNA chaperones and their regulons .............. 188
   Summary .................................................... 190
6  DNA Methylation in Bacteria: A Case for Bacterial
   Epigenetics ................................................ 191
   6.1  Introduction .......................................... 191
   6.2  DNA methyltransferases in bacteria: From
        restriction-modification systems ...................... 192
   6.3  Identifying sites of DNA methylation on a genomic
        scale ................................................. 195
        6.3.1  Methylated DNA immunoprecipitation ............. 195
        6.3.2  Bisulphite sequencing .......................... 195
        6.3.3  DNA cytosine methylation in laboratory
               E. coli ........................................ 197
   6.4  Detecting DNA methylation by single-molecule real-
        time sequencing ....................................... 200
        6.4.1  DNA adenine methylation in pathogenic E. coli
               by SMRT sequencing ............................. 202
        6.4.2  Insight into the epigenetic control of
               Caulobacter crescentus cell cycle from SMRT
               sequencing ..................................... 203
Summary ....................................................... 205
Index ......................................................... 207

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